protected override void Context()
{
base.Context();
_newName = "TOTO";
_f1 = new ExplicitFormula("A+B");
_f2 = new ExplicitFormula("A+B");
_f3 = new ExplicitFormula("A+B");
_f1.AddObjectPath(new FormulaUsablePath(_initialSimulationName, "Liver", "Cell"));
_f1.AddObjectPath(new FormulaUsablePath("Drug", "LogP"));
_f2.AddObjectPath(new FormulaUsablePath("SU", "Liver", "Cell"));
_f2.AddObjectPath(new FormulaUsablePath("Drug", "LogP"));
_f3.AddObjectPath(new FormulaUsablePath(_initialSimulationName, "Liver", "Cell"));
_f3.AddObjectPath(new FormulaUsablePath(_initialSimulationName, "LogP"));
var p1 = new PKSimParameter().WithName("P1").WithFormula(_f1);
var p2 = new PKSimParameter().WithName("P2").WithFormula(_f2);
var p3 = new PKSimParameter().WithName("P3").WithFormula(_f3);
var c1 = new Container().WithName("C1");
c1.Add(p3);
_root.Add(p1);
_root.Add(p2);
_root.Add(c1);
var results = new SimulationResults {
Time = new QuantityValues {
ColumnId = "0", QuantityPath = "baseGrid"
}
};
_individualResults = new IndividualResults {
IndividualId = 1
};
results.Add(_individualResults);
var quantityCache = new PathCacheForSpecs <IQuantity>
{
{ "Liver|Cell|Drug", new MoleculeAmount {
QuantityType = QuantityType.Drug
} },
{ "Liver|Cell|Meta", new MoleculeAmount {
QuantityType = QuantityType.Metabolite
} },
};
_individualResults.Add(new QuantityValues {
PathList = new[] { "Liver", "Cell", "Drug" }.ToList()
});
_individualResults.Add(new QuantityValues {
PathList = new[] { "Liver", "Cell", "Meta" }.ToList()
});
_individualSimulation.Results = results;
_individualSimulation.DataRepository = new DataRepository();
_individualSimulation.Reactions = new ReactionBuildingBlock();
_individualSimulation.SimulationSettings = new SimulationSettings();
A.CallTo(_containerTask).WithReturnType <PathCache <IQuantity> >().Returns(quantityCache);
A.CallTo(() => _curveNamer.RenameCurvesWithOriginalNames(_individualSimulation, A <Action> ._, true)).Invokes(x => x.Arguments[1].DowncastTo <Action>()());
}
public SimulationResults CreateResultsFrom(DataRepository dataRepository)
{
if (dataRepository.IsNull())
{
return(new NullSimulationResults());
}
var results = new SimulationResults();
var baseGrid = dataRepository.BaseGrid;
results.Time = valuesFrom(baseGrid);
foreach (var columnsForIndividual in dataRepository.AllButBaseGrid().GroupBy(selectIndividualIndex))
{
var individualResults = new IndividualResults {
IndividualId = columnsForIndividual.Key, Time = results.Time
};
foreach (var dataColumn in columnsForIndividual)
{
individualResults.Add(valuesFrom(dataColumn, pathWithoutIndividualIndex(dataColumn, columnsForIndividual.Key)));
}
individualResults.UpdateQuantityTimeReference();
results.Add(individualResults);
}
return(results);
}
private SimulationResults createResultsFrom(DataRepository dataRepository, ISimModelBatch simModel, string[] parameters)
{
if (dataRepository.IsNull() || dataRepository.BaseGrid == null)
{
return(new NullSimulationResults());
}
var results = new SimulationResults {
Time = valuesFrom(dataRepository.BaseGrid, null, new string[] { })
};
foreach (var columnsForIndividual in dataRepository.AllButBaseGrid().GroupBy(selectIndividualIndex))
{
var individualResults = new IndividualResults {
IndividualId = columnsForIndividual.Key, Time = results.Time
};
foreach (var dataColumn in columnsForIndividual)
{
individualResults.Add(valuesFrom(dataColumn, pathWithoutIndividualIndex(dataColumn, columnsForIndividual.Key), simModel, parameters));
}
individualResults.UpdateQuantityTimeReference();
results.Add(individualResults);
}
return(results);
}
/// <summary>
/// Add results for successfull individual
/// </summary>
/// <param name="individualResults"></param>
public void Add(IndividualResults individualResults)
{
Results.Add(individualResults);
var runInfo = new IndividualRunInfo {
Success = true
};
_individualRunInfos[individualResults.IndividualId] = runInfo;
}
protected override void Context()
{
base.Context();
_newName = "TOTO";
_f1 = new ExplicitFormula("A+B");
_f2 = new ExplicitFormula("A+B");
_f3 = new ExplicitFormula("A+B");
_f1.AddObjectPath(new FormulaUsablePath(_initialSimulationName, "Liver", "Cell"));
_f1.AddObjectPath(new FormulaUsablePath("Drug", "LogP"));
_f2.AddObjectPath(new FormulaUsablePath("SU", "Liver", "Cell"));
_f2.AddObjectPath(new FormulaUsablePath("Drug", "LogP"));
_f3.AddObjectPath(new FormulaUsablePath(_initialSimulationName, "Liver", "Cell"));
_f3.AddObjectPath(new FormulaUsablePath(_initialSimulationName, "LogP"));
var p1 = new PKSimParameter().WithName("P1").WithFormula(_f1);
var p2 = new PKSimParameter().WithName("P2").WithFormula(_f2);
var p3 = new PKSimParameter().WithName("P3").WithFormula(_f3);
var c1 = new Container().WithName("C1");
c1.Add(p3);
_root.Add(p1);
_root.Add(p2);
_root.Add(c1);
var results = new SimulationResults {
Time = new QuantityValues {
ColumnId = "0", QuantityPath = "baseGrid"
}
};
_individualResults = new IndividualResults {
IndividualId = 1
};
results.Add(_individualResults);
var quantityCache = new PathCacheForSpecs <IQuantity>
{
{ "Liver|Cell|Drug", new MoleculeAmount {
QuantityType = QuantityType.Drug
} },
{ "Liver|Cell|Meta", new MoleculeAmount {
QuantityType = QuantityType.Metabolite
} },
};
_individualResults.Add(new QuantityValues {
PathList = new[] { "Liver", "Cell", "Drug" }.ToList()
});
_individualResults.Add(new QuantityValues {
PathList = new[] { "Liver", "Cell", "Meta" }.ToList()
});
_individualSimulation.Results = results;
A.CallTo(_containerTask).WithReturnType <PathCache <IQuantity> >().Returns(quantityCache);
}
public static SimulationResults CreateSimulationResults(int numberOfIndividuals = 10, int numberOfPaths = 5, int numberOfPoints = 100)
{
var populationResults = new SimulationResults {
Time = createTimeArray(numberOfPoints)
};
for (int i = 0; i < numberOfIndividuals; i++)
{
var results = newIndividualResults(i, numberOfPaths, numberOfPoints);
populationResults.Add(results);
results.Time = populationResults.Time;
results.UpdateQuantityTimeReference();
}
return(populationResults);
}
protected override void Context()
{
base.Context();
var results = new SimulationResults {
Time = new QuantityValues {
ColumnId = "0", QuantityPath = "baseGrid"
}
};
_individualResults = new IndividualResults {
IndividualId = 1
};
results.Add(_individualResults);
_quantityCache = new PathCacheForSpecs <IQuantity>
{
{ "C|Liver|Cell|C2", new MoleculeAmount {
QuantityType = QuantityType.Drug
} },
{ "C|Liver|Cell|Meta", new MoleculeAmount {
QuantityType = QuantityType.Metabolite
} }
};
_individualResults.Add(new QuantityValues {
ColumnId = "1", PathList = new[] { "C", "Liver", "Cell", "C" }.ToList()
});
_individualResults.Add(new QuantityValues {
ColumnId = "3", PathList = new[] { "C", "Liver", "Cell", "Meta" }.ToList()
});
_individualResults.Add(new QuantityValues {
ColumnId = "4", PathList = new[] { "S", "Liver", "Cell" }.ToList()
});
A.CallTo(_containerTask).WithReturnType <PathCache <IQuantity> >().Returns(_quantityCache);
_individualSimulation.Results = results;
}
